Err... really? I don't think I've over-leveled my characters, since they have an average of 29, and my three who fought the last boss had an average of 31..
The one difficult turn-based RPG I've recently played would be Shin Megami Tensei: Nocturne, especially on hard mode. Even on normal, random encounters can easily make your game over if you don't know what you're doing.
Don't get me wrong though, Xenosaga is a great RPG, and it is not super easy or anything.
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